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Nature Medicine 2014, Vol. 20 (12) :1479 -14795 doi:10.1038/nm.3729 <<-上一篇 下一篇 ->>
Anchored multiplex FOR for targeted next-generation sequencing
Zheng, Zongli;Liebers, Matthew;Zhelyazkova, Boryana;Cao, Yi;Panditi, Divya;Lynch, Kerry D.;Chen, Juxiang;Robinson, Hayley E.;Shim, Hyo Sup;Chmielecki, Juliann;Pao, William;Engelman, Jeffrey A.;Iafrate, A. John;Le, Long Phi
[Zheng, Zongli; Liebers, Matthew; Zhelyazkova, Boryana; Cao, Yi; Panditi, Divya; Lynch, Kerry D.; Chen, Juxiang; Robinson, Hayley E.; Shim, Hyo Sup; Iafrate, A. John; Le, Long Phi] Massachusetts Gen Hosp, Dept Pathol, Boston, MA 02114 USA.;[Zheng, Zongli] Karolinska Inst, Dept Med Epidemiol & Biostat, Stockholm, Sweden.;[Chen, Juxiang] Shanghai Changzheng Hosp, Dept Neurosurg, Shanghai, Peoples R China.;[Shim, Hyo Sup] Yonsei Univ, Coll Med, Dept Pathol, Seoul, South Korea.;[Chmielecki, Juliann; Pao, William] Vanderbilt Univ, Med Ctr, Nashville, TN USA.;[Engelman, Jeffrey A.; Iafrate, A. John; Le, Long Phi] Massachusetts Gen Hosp, Ctr Canc, Boston, MA USA.
Abstract: We describe a rapid target enrichment method for next-generation sequencing, termed anchored multiplex PCR (AMP), that is compatible with low nucleic acid input from formalin-fixed paraffin-embedded (FFPE) specimens. AMP is effective in detecting gene rearrangements (without prior knowledge of the fusion partners), single nucleotide variants, insertions, deletions and copy number changes. Validation of a gene rearrangement panel using 319 FFPE samples showed 100% sensitivity (95% confidence limit: 96.5-100%) and 100% specificity (95% confidence limit: 99.3-100%) compared with reference assays. On the basis of our experience with performing AMP on 986 clinical FFPE samples, we show its potential as both a robust clinical assay and a powerful discovery tool, which we used to identify new therapeutically important gene fusions: ARHGEF2-NTRK1 and CHTOP-NTRK1 in glioblastoma, MSN-ROS1, TRIM4-BRAF, VAMP2-NRG1, TPM3-NTRK1 and RUFY2-RET in lung cancer, FGFR2-CREB5 in cholangiocarcinoma and PPL-NTRK1 in thyroid carcinoma. AMP is a scalable and efficient next-generation sequencing target enrichment method for research and clinical applications.
Keywords: CELL LUNG-CANCER PCR GENOMES DNA ENRICHMENT DISCOVERY VARIANTS FUSIONS TUMORS ROS1
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